We are going to need more information about how your have the PMDX boards wired and configured. I'll start off with a couple of questions and some things to look at:
So you have 2 parallel ports in your PC - one connected to the PMDX-132 and one connected to the PMDX-122, is that correct?
Do you have the PMDx-132 and 122 configured like figure 3 in the PMDX-132 manual, including the jumper settings? If not, please describe (or post a drawing) of haw they are connected and configured.
If not, are the PMDX-132 and PMDX-122 configured to pay attention to the "charge pump" signal? On the 132 this is jumper JP1, which can be either "not EStop" or "CP OK". On the 122 this is jumper JP3 and can be either "not EStop/Fault" or "CP-OK and not EStop/Fault".
When the motion stops, look at the "outputs enabled" LEDs on both of the PMDX boards. Are these LEDs on or off?
When the motion stops (and LinuxCNC still thinks it is outputting step pulses), do the inputs work (limit switches, EStop, etc.)?
And one last question - when the motion stops, can you change any of the outputs signals? I don't know if LinuxCNC will allow you manual control of any output while it is running a GCode program, and I don't know what outputs you have defined- spindle on? coolant on? Some external indicator light? So this may not be possible to test.
Bob